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<big><strong><span class="block">&nbsp;HardMask.pl</span></strong></big>
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	<li><a href="#name">NAME</a></li>
	<li><a href="#synopsis">SYNOPSIS</a></li>
	<li><a href="#description">DESCRIPTION</a></li>
	<li><a href="#arguments">ARGUMENTS</a></li>
	<li><a href="#author">AUTHOR</a></li>
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<h1><a name="name">NAME</a></h1>
<p>HardMask.pl - Hard mask soft masked fasta files.</p>
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<h1><a name="synopsis">SYNOPSIS</a></h1>
<pre>
   HardMask.pl -i InFile.fasta -o OutFile.fasta -m X</pre>
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<h1><a name="description">DESCRIPTION</a></h1>
<p>Given a soft masked fasta file, replace all lowercase
characters with a single mask character. The character that is
used for masking is a variable the user can select using the -m flag.</p>
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<h1><a name="arguments">ARGUMENTS</a></h1>
<dl>
<dt><strong><a name="item_%2di_infile%2efasta">-i InFile.fasta</a></strong><br />
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<dd>
Path to the input fasta file
</dd>
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<dt><strong><a name="item_%2do_outfile%2efasta">-o OutFile.fasta</a></strong><br />
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<dd>
Path to the output fasta file. The default is output is: InFile.hard.masked
</dd>
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<dt><strong><a name="item_%2dm_x">-m X</a></strong><br />
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<dd>
The character to mask with. The default value is 'N'. Valid values
are: N,n,X,x.
</dd>
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<h1><a name="author">AUTHOR</a></h1>
<p>James C. Estill &lt;JamesEstill at gmail.com&gt;</p>
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<big><strong><span class="block">&nbsp;HardMask.pl</span></strong></big>
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